First record of a tandem-repeat region within the mitochondrial genome of Clonorchis sinensis using a long-read sequencing approach

New mitogenomes of Runcinidae and Facelinidae: two understudied heterobranch families (Mollusca: Gastropoda)

Here, we present the mitochondrial sequences of two sea slugs (Heterobranchia): Runcina aurata and Facelina auriculata, the latter being the type species of the family. The mitochondrial genomes are 14,282 and 14,171bp in length, respectively, with a complete set of 13 PCGs, 2 rRNAs, and 22 tRNAs. None of the mitogenomes show gene reorganization, keeping the standard mitogenomic structure of Heterobranchia. Nucleotide composition differs significantly between them, with R. aurata showing the most AT-rich mitogenome (25.7% GC content) reported to date in Heterobranchia, and F. auriculata showing a rich GC content (35%) compared with other heterobranch mitochondrial genomes.

The invasive land flatworm Arthurdendyus triangulatus has repeated sequences in the mitogenome, extra-long cox2 gene and paralogous nuclear rRNA clusters

Using a combination of short- and long-reads sequencing, we were able to sequence the complete mitochondrial genome of the invasive 'New Zealand flatworm' Arthurdendyus triangulatus (Geoplanidae, Rhynchodeminae, Caenoplanini) and its two complete paralogous nuclear rRNA gene clusters. The mitogenome has a total length of 20,309 bp and contains repetitions that includes two types of tandem-repeats that could not be solved by short-reads sequencing. We also sequenced for the first time the mitogenomes of four species of Caenoplana (Caenoplanini). A maximum likelihood phylogeny associated A. triangulatus with the other Caenoplanini but Parakontikia ventrolineata and Australopacifica atrata were rejected from the Caenoplanini and associated instead with the Rhynchodemini, with Platydemus manokwari. It was found that the mitogenomes of all species of the subfamily Rhynchodeminae share several unusual structural features, including a very long cox2 gene. This is the first time that the complete paralogous rRNA clusters, which differ in length, sequence and seemingly number of copies, were obtained for a Geoplanidae.

Whole-genome sequence of the Cooley spruce gall adelgid, Adelges cooleyi (Hemiptera: Sternorrhyncha: Adelgidae)

The adelgids (Adelgidae) are a small family of sap-feeding insects, which, together with true aphids (Aphididae) and phylloxerans (Phylloxeridae), make up the infraorder Aphidomorpha. Some adelgid species are highly destructive to forest ecosystems such as Adelges tsugae, Adelges piceae, Adelges laricis, Pineus pini, and Pineus boerneri. Despite this, there are no high-quality genomic resources for adelgids, hindering advanced genomic analyses within Adelgidae and among Aphidomorpha. Here, we used PacBio continuous long-read and Illumina RNA-sequencing to construct a high-quality draft genome assembly for the Cooley spruce gall adelgid, Adelges cooleyi (Gillette), a gall-forming species endemic to North America. The assembled genome is 270.2 Mb in total size and has scaffold and contig N50 statistics of 14.87 and 7.18 Mb, respectively. There are 24,967 predicted coding sequences, and the assembly completeness is estimated at 98.1 and 99.6% with core BUSCO gene sets of Arthropoda and Hemiptera, respectively. Phylogenomic analysis using the A. cooleyi genome, 3 publicly available adelgid transcriptomes, 4 phylloxera transcriptomes, the Daktulosphaira vitifoliae (grape phylloxera) genome, 4 aphid genomes, and 2 outgroup coccoid genomes fully resolves adelgids and phylloxerans as sister taxa. The mitochondrial genome is 24 kb, among the largest in insects sampled to date, with 39.4% composed of noncoding regions. This genome assembly is currently the only genome-scale, annotated assembly for adelgids and will be a valuable resource for understanding the ecology and evolution of Aphidomorpha.

Characterization of the Complete Mitochondrial Genome and Phylogenetic Analyses of Eurytrema coelomaticum (Trematoda: Dicrocoeliidae)

Eurytrema coelomaticum, a pancreatic fluke, is recognized as a causative agent of substantial economic losses in ruminants. This infection, commonly referred to as eurytrematosis, is a significant concern due to its detrimental impact on livestock production. However, there is a paucity of knowledge regarding the mitochondrial genome of E. coelomaticum. In this study, we performed the initial sequencing of the complete mitochondrial genome of E. coelomaticum. Our findings unveiled that the mitochondrial genome of E. coelomaticum spans a length of 15,831 bp and consists of 12 protein-coding genes, 22 tRNA genes, two rRNA genes, and two noncoding regions. The A+T content constituted 62.49% of the genome. Moreover, all 12 protein-coding genes of E. coelomaticum exhibit the same arrangement as those of E. pancreaticum and other published species belonging to the family Dicrocoeliidae. The presence of a short string of additional amino acids (approximately 20~23 aa) at the N-terminal of the cox1 protein in both E. coelomaticum and E. pancreaticum mitochondrial genomes has contributed to the elongation of the cox1 gene in genus Eurytrema, surpassing that of all previously sequenced Dicrocoeliidae. The phylogenetic analysis displayed a close relationship between E. coelomaticum and E. pancreaticum, along with a genus-level association between Eurytrema and Lyperosomum. These findings underscore the importance of mitochondrial genomic data for comparative studies of Dicrocoeliidae and even Digenea, offering valuable DNA markers for future investigations in the systematic, epidemiological, and population genetic studies of this parasite and other digenean trematodes.

Current status and progress in the omics of Clonorchis sinensis

Clonorchis sinensis (C. sinensis) is a fish-borne trematode that inhabits the bile duct of mammals including humans, cats, dogs, rats, and so on. In the complex life cycle of C. sinensis, the worm develops successively in two intermediate hosts in fresh water and one definitive host. What's more, it undergoes eight developmental stages with a distinct morphology. Clonorchiasis, caused by C. sinensis infection, is an important food-borne parasitic disease and one of the most common zoonoses. C. sinensis infection could result in hyperplasia of the bile duct epithelium, obstructive jaundice, gall-stones, cholecystitis and cholangitis, even liver cirrhosis and cholangiocarcinoma. Thus, clonorchiasis is a serious public health problem in endemic areas. Integrated strategies should be adopted in the prevention and control of clonorchiasis due to the epidemiological characteristics. The recent advances in high-throughput technologies have made available the profiling of multiple layers of a biological system, genomics, transcriptomics, proteomics, and metabolomics. These data can help us to get more information about the development, physiology, metabolism, and reproduction of the parasite as well as pathogenesis and parasite-host interactions in clonorchiasis. In the present study, we summarized recent progresses in omics studies on C. sinensis providing insights into the studies and future directions on treating and preventing C. sinensis associated diseases.

Molecular Phylogeny of Thoracotreme Crabs Including Nine Newly Determined Mitochondrial Genomes

Mitochondrial genomes are used widely for the molecular phylogenetic analysis of animals. Although phylogenetic analyses based on the mitogenomes of brachyurans often yield well-resolved phylogenies, most interfamilial phylogenetic relationships in Thoracotremata remain unclear. We determined nine new mitogenomes of Thoracotremata, including mitogenomes of Camptandriidae (Deiratonotus japonicus), Dotillidae (Ilyoplax integra, Ilyoplax pusilla, and Tmethypocoelis choreutes), Macrophthalmidae (Ilyograpsus nodulosus), Pinnotheridae (Arcotheres sp. and Indopinnixa haematosticta), Plagusiidae (Guinusia dentipes), and Percnidae (Percnon planissimum). Interestingly, Percnon planissimum (Percnidae) was found to possess ≥ 19 repeated sequences in the control region. The gene orders of Il. nodulosus, Arcotheres sp., and In. haematosticta were revealed to be unique among thoracotreme crabs. Although the results of Bayesian and maximum likelihood (ML) phylogenetic analyses of three datasets were incongruent, highly supported clades (PP ≥ 0.99 or BS ≥ 99%) were not contradictory among the analyses. All analyses suggested the paraphyly of Grapsoidea and Ocypodoidea, corroborating the findings of previous studies based on molecular phylogenies of thoracotreme crabs. The phylogenetic positions of symbiotic thoracotreme crabs, Pinnotheridae and Cryptochiridae, were highly supported (Pinnotheridae + Ocypodidae and Cryptochiridae + Grapsidae, respectively) for the Bayesian analyses but not for the ML analyses. Analyses of more thoracotreme species' mitogenome sequences in additional studies will further strengthen the framework for thoracotreme evolution.

Novel mitochondrial genome rearrangements including duplications and extensive heteroplasmy could underlie temperature adaptations in Antarctic notothenioid fishes

Mitochondrial genomes are known for their compact size and conserved gene order, however, recent studies employing long-read sequencing technologies have revealed the presence of atypical mitogenomes in some species. In this study, we assembled and annotated the mitogenomes of five Antarctic notothenioids, including four icefishes (Champsocephalus gunnari, C. esox, Chaenocephalus aceratus, and Pseudochaenichthys georgianus) and the cold-specialized Trematomus borchgrevinki. Antarctic notothenioids are known to harbor some rearrangements in their mt genomes, however the extensive duplications in icefishes observed in our study have never been reported before. In the icefishes, we observed duplications of the protein coding gene ND6, two transfer RNAs, and the control region with different copy number variants present within the same individuals and with some ND6 duplications appearing to follow the canonical Duplication-Degeneration-Complementation (DDC) model in C. esox and C. gunnari. In addition, using long-read sequencing and k-mer analysis, we were able to detect extensive heteroplasmy in C. aceratus and C. esox. We also observed a large inversion in the mitogenome of T. borchgrevinki, along with the presence of tandem repeats in its control region. This study is the first in using long-read sequencing to assemble and identify structural variants and heteroplasmy in notothenioid mitogenomes and signifies the importance of long-reads in resolving complex mitochondrial architectures. Identification of such wide-ranging structural variants in the mitogenomes of these fishes could provide insight into the genetic basis of the atypical icefish mitochondrial physiology and more generally may provide insights about their potential role in cold adaptation.

Mitogenomic and nuclear ribosomal transcription unit datasets support the synonymy of Paragonimus iloktsuenensis and P. ohirai (Paragonimidae: Platyhelminthes)

The complete mitogenome (mtDNA) of nominal Paragonimus iloktsuenensis (Paragonimidae: Trematoda) and the nuclear ribosomal transcription unit (rTU) coding region (rTU*: from 5'-terminus of 18S to 3'-terminus of 28S rRNA gene, excluding the external spacer region) of this species and of P. ohirai were obtained and used to further support the previously suggested synonymy of these taxa in the P. ohirai complex. The complete mitogenome of P. iloktsuenensis was 14,827 bp long (GenBank: ON961029) and nearly identical to that of P. ohirai (14,818 bp; KX765277), with a 99.12% nucleotide identity. The rTU* was 7543 bp and 6932 bp in these two taxa, respectively. All genes and spacers in the rTU were identical in length, with exception of the first internal transcribed spacer, which contained multiple tandem repeat units (6.7 for P. iloktsuenensis and 5.7 for P. ohirai). There was near 100% identity for the rTU genes. The phylogenetic topology inferred from the mtDNA and from individual gene regions (partial cox1 of 387 bp and the ITS-2 of 282 bp - 285 bp) indicated a very close relationship consistent with synonymy of P. iloktsuenensis and P. ohirai. The datasets provided here will be useful for taxonomic reappraisal as well as studies of evolutionary and population genetics of the genus Paragonimus and family Paragonimidae.

The complete mitogenome of the Asian lung fluke Paragonimus skrjabini miyazakii and its implications for the family Paragonimidae (Trematoda: Platyhelminthes)

The complete circular mitogenome of Paragonimus skrjabini miyazakii (Platyhelminthes: Paragonimidae) from Japan, obtained by PacBio long-read sequencing, was 17 591 bp and contained 12 protein-coding genes (PCGs), 2 mitoribosomal RNA and 22 transfer RNA genes. The atp8 gene was absent, and there was a 40 bp overlap between nad4L and nad4. The long non-coding region (4.3 kb) included distinct types of long and short repeat units. The pattern of base usage for PCGs and the mtDNA coding region overall in Asian and American Paragonimus species (P. s. miyazakii, P. heterotremus, P. ohirai and P. kellicotti) and the Indian form of P. westermani was T > G > A > C. On the other hand, East-Asian P. westermani used T > G > C > A. Five Asian and American Paragonimus species and P. westermani had TTT/Phe, TTG/Leu and GTT/Val as the most frequently used codons, whereas the least-used codons were different in each species and between regional forms of P. westermani. The phylogenetic tree reconstructed from a concatenated alignment of amino acids of 12 PCGs from 36 strains/26 species/5 families of trematodes confirmed that the Paragonimidae is monophyletic, with 100% nodal support. Paragonimus skrjabini miyazakii was resolved as a sister to P. heterotremus. The P. westermani clade was clearly separate from remaining congeners. The latter clade was comprised of 2 subclades, one of the East-Asian and the other of the Indian Type 1 samples. Additional mitogenomes in the Paragonimidae are needed for genomic characterization and are useful for diagnostics, identification and genetic/ phylogenetic/ epidemiological/ evolutionary studies of the Paragonimidae.

Mitochondrial genome of Bulinus truncatus (Gastropoda: Lymnaeoidea): Implications for snail systematics and schistosome epidemiology

Many freshwater snails of the genus Bulinus act as intermediate hosts in the life-cycles of schistosomes in Africa and adjacent regions. Currently, 37 species of Bulinus representing four groups are recognised. The mitochondrial cytochrome c oxidase subunit 1 (cox1) gene has shown utility for identifying and differentiating Bulinus species and groups, but taxonomic relationships based on genetic data are not entirely consistent with those inferred using morphological and biological features. To underpin future systematic studies of members of the genus, we characterised here the mitochondrial genome of Bulinus truncatus (from a defined laboratory strain) using a combined second- and third-generation sequencing and informatics approach, enabling taxonomic comparisons with other planorbid snails for which mitochondrial (mt) genomes were available. Analyses showed consistency in gene order and length among mitochondrial genomes of representative planorbid snails, with the lowest and highest nucleotide diversities being in the cytochrome c oxidase and nicotinamide dehydrogenase subunit genes, respectively. This first mt genome for a representative of the genus Bulinus should provide a useful resource for future investigations of the systematics, population genetics, epidemiology and/or ecology of Bulinus and related snails. The sequencing and informatic workflow employed here should find broad applicability to a range of other snail intermediate hosts of parasitic trematodes.

PNA microprobe for label-free detection of expanded trinucleotide repeats

We present a PNA microprobe sensing platform to detect trinucleotide repeat mutation by electrochemical impedance spectroscopy. The microprobe platform discriminated Huntington's disease-associated CAG repeats in cell-derived total RNA with S/N 1 : 3. This sensitive, label-free, and PCR-free detection strategy may be employed in the future to develop biosensing platforms for the detection of a plethora of repeat expansion disorders.

Mitophylogenomics of the zoonotic fluke Echinostoma malayanum confirms it as a member of the genus Artyfechinostomum Lane, 1915 and illustrates the complexity of Echinostomatidae systematics

The complete mitochondrial genome (mitogenome or mtDNA) of the trematode Echinostoma malayanum Leiper, 1911 was fully determined and annotated. The circular mtDNA molecule comprised 12 protein-coding genes (PCGs) (cox1 - 3, cob, nad1 - 6, nad4L, atp6), two mitoribosomal RNAs (MRGs) (16S or rrnL and 12S or rrnS), and 22 transfer RNAs (tRNAs or trn), and a non-coding region (NCR) rich in long and short tandem repeats (5.5 LRUs/336 bp/each and 7.5 SRUs/207 bp/each). The atp8 gene is absent and the 3' end of nad4L overlaps the 5' end of nad4 by 40 bp. Special DHU-arm missing tRNAs for Serine were found for both tRNA^Ser1(AGN) and tRNA^Ser2(UCN). Codons of TTT (for phenylalanine), TTG (for leucine), and GTT (for valine) were the most, and CGC (for Arginine) was the least frequently used. A similar usage pattern was seen in base composition, AT and GC skewness for PCGs, MRGs, and mtDNA* (coding cox3 to nad5) in E. malayanum and Echinostomatidae. The nucleotide use is characterized by (T > G > A > C) for PCGs/mtDNA*, and by (T > G ≈ A > C) for MRGs. E. malayanum exhibited the lowest genetic distance (0.53%) to Artyfechinostomum sufrartyfex, relatively high to the Echinostoma congeners (13.20-13.99%), higher to Hypoderaeum conoideum (16.18%), and the highest to interfamilial Echinochasmidae (26.62%); Cyclocoelidae (30.24%); and Himasthlidae (25.36%). Topology indicated the monophyletic position between E. malayanum/A. sufrartyfex and the group of Echinostoma caproni, Echinostoma paraensei, Echinostoma miyagawai, and Echinostoma revolutum, rendering Hypoderaeum conoideum and unidentified Echinostoma species paraphyletic. The strictly closed genomic/taxonomic/phylogenetic features (including base composition, skewness, codon usage/bias, genetic distance, and topo-position) reinforced Echinostoma malayanum to retake its generic validity within the Artyfechinostomum genus.

Hammerhead flatworms (Platyhelminthes, Geoplanidae, Bipaliinae): mitochondrial genomes and description of two new species from France, Italy, and Mayotte

BACKGROUND

New records of alien land planarians are regularly reported worldwide, and some correspond to undescribed species of unknown geographic origin. The description of new species of land planarians (Geoplanidae) should classically be based on both external morphology and histology of anatomical structures, especially the copulatory organs, ideally with the addition of molecular data.

METHODS

Here, we describe the morphology and reproductive anatomy of a species previously reported as Diversibipalium "black", and the morphology of a species previously reported as Diversibipalium "blue". Based on next generation sequencing, we obtained the complete mitogenome of five species of Bipaliinae, including these two species.

RESULTS

The new species Humbertium covidum n. sp. (syn: Diversibipalium "black" of Justine et al., 2018) is formally described on the basis of morphology, histology and mitogenome, and is assigned to Humbertium on the basis of its reproductive anatomy. The type-locality is Casier, Italy, and other localities are in the Department of Pyrénées-Atlantiques, France; some published or unpublished records suggest that this species might also be present in Russia, China, and Japan. The mitogenomic polymorphism of two geographically distinct specimens (Italy vs France) is described; the cox1 gene displayed 2.25% difference. The new species Diversibipalium mayottensis n. sp. (syn: Diversibipalium "blue" of Justine et al., 2018) is formally described on the basis of external morphology and complete mitogenome and is assigned to Diversibipalium on the basis of an absence of information on its reproductive anatomy. The type- and only known locality is the island of Mayotte in the Mozambique Channel off Africa. Phylogenies of bipaliine geoplanids were constructed on the basis of SSU, LSU, mitochondrial proteins and concatenated sequences of cox1, SSU and LSU. In all four phylogenies, D. mayottensis was the sister-group to all the other bipaliines. With the exception of D. multilineatum which could not be circularised, the complete mitogenomes of B. kewense, B. vagum, B. adventitium, H. covidum and D. mayottensis were colinear. The 16S gene in all bipaliine species was problematic because usual tools were unable to locate its exact position.

CONCLUSION

Next generation sequencing, which can provide complete mitochondrial genomes as well as traditionally used genes such as SSU, LSU and cox1, is a powerful tool for delineating and describing species of Bipaliinae when the reproductive structure cannot be studied, which is sometimes the case of asexually reproducing invasive species. The unexpected position of the new species D. mayottensis as sister-group to all other Bipaliinae in all phylogenetic analyses suggests that the species could belong to a new genus, yet to be described.

The complete mitochondrial genome sequences of the cat flea Ctenocephalides felis felis (Siphonaptera: Pulicidae) support the hypothesis that C. felis isolates from China and USA were the same C. f. felis subspecies

The cat flea Ctenocephalides felis (Siphonaptera: Pulicidae) is the most important ectoparasite in cats and dogs worldwide. Over the years, there has been much dispute regarding the taxonomic and systematic status of C. felis. Mitochondrial (mt) genome sequences are useful genetic markers for the identification and differentiation of ectoparasites, but the mt genome of C. felis and its subspecies has not yet been entirely characterized. In the present study, the entire mt genome of C. f. felis from China was sequenced and compared with that of C. felis from the USA. Both contain 37 genes and a long non-coding region of >6 kbp. The molecular identity between the Chinese and American isolates was 99%, except for the non-coding region. The protein-coding genes showed differences at both the nucleotide (1.2%) and amino acid (1%) levels. Interestingly, the cox1 gene of the Chinese isolate had an unusual putative start codon (TTT). Taken together, our analyses strongly support the hypothesis that C. felis isolates from China and the USA were the same C. f. felis subspecies. The mt genome sequence of the C. f. felis China isolate presented in this study provides useful molecular markers to further address the taxonomy and systematics of C. felis.

High-quality reference genome for Clonorchis sinensis

The Chinese liver fluke, Clonorchis sinensis, causes the disease clonorchiasis, affecting ~35 million people in regions of China, Vietnam, Korea and the Russian Far East. Chronic clonorchiasis causes cholangitis and can induce a malignant cancer, called cholangiocarcinoma, in the biliary system. Control in endemic regions is challenging, and often relies largely on chemotherapy with one anthelmintic, called praziquantel. Routine treatment carries a significant risk of inducing resistance to this anthelmintic in the fluke, such that the discovery of new interventions is considered important. It is hoped that the use of molecular technologies will assist this endeavour by enabling the identification of drug or vaccine targets involved in crucial biological processes and/or pathways in the parasite. Although draft genomes of C. sinensis have been published, their assemblies are fragmented. In the present study, we tackle this genome fragmentation issue by utilising, in an integrated way, advanced (second- and third-generation) DNA sequencing and informatic approaches to build a high-quality reference genome for C. sinensis, with chromosome-level contiguity and curated gene models. This substantially-enhanced genome provides a resource that could accelerate fundamental and applied molecular investigations of C. sinensis, clonorchiasis and/or cholangiocarcinoma, and assist in the discovery of new interventions against what is a highly significant, but neglected disease-complex.

Nanopore Sequencing Resolves Elusive Long Tandem-Repeat Regions in Mitochondrial Genomes

Long non-coding, tandem-repetitive regions in mitochondrial (mt) genomes of many metazoans have been notoriously difficult to characterise accurately using conventional sequencing methods. Here, we show how the use of a third-generation (long-read) sequencing and informatic approach can overcome this problem. We employed Oxford Nanopore technology to sequence genomic DNAs from a pool of adult worms of the carcinogenic parasite, Schistosoma haematobium, and used an informatic workflow to define the complete mt non-coding region(s). Using long-read data of high coverage, we defined six dominant mt genomes of 33.4 kb to 22.6 kb. Although no variation was detected in the order or lengths of the protein-coding genes, there was marked length (18.5 kb to 7.6 kb) and structural variation in the non-coding region, raising questions about the evolution and function of what might be a control region that regulates mt transcription and/or replication. The discovery here of the largest tandem-repetitive, non-coding region (18.5 kb) in a metazoan organism also raises a question about the completeness of some of the mt genomes of animals reported to date, and stimulates further explorations using a Nanopore-informatic workflow.